Locus 2478

Sequence ID 3L_DroMel_CAF1
Location 6,976,952 – 6,977,135
Length 183
Max. P 0.984680
window3832 window3833 window3834 window3835

overview

Window 2

Location 6,976,952 – 6,977,055
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.04
Mean single sequence MFE -28.17
Consensus MFE -21.13
Energy contribution -20.45
Covariance contribution -0.69
Combinations/Pair 1.21
Mean z-score -2.41
Structure conservation index 0.75
SVM decision value 1.92
SVM RNA-class probability 0.982567
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6976952 103 + 23771897
CUUUGAACGCGUGCGCAACGCAAGCCGUUUAAUCUGAAUUUGCUCACUCAAUGUGGGCUGGAAUAUAUAU-------UAUAUGUAUA----------UAUAUAUUCAUUUUCGGCCACUA
..((((((((.((((...)))).).))))))).(((((...((((((.....))))))..((((((((((-------.........)----------)))))))))...)))))...... ( -29.30)
>DroSim_CAF1 46638 110 + 1
CUUUGAACGCGUGCGCAAUGCAACCCGUUUAAUCUAAAUUUGUUCACUCAAUGUGGGCUGGAAUAUAUAUAUAUAUUGAUUUAUAUG----------UAUAUAUUCAUUUUCGGCCACUA
..(((((((..(((.....)))...)))))))............(((.....)))((((((((((((((((((((......))))))----------))))))))).....))))).... ( -31.50)
>DroEre_CAF1 46798 112 + 1
CUUUGAACGCGUGCGCAACGCAACCUGUUUAAUCUGAAUUUGCUCACCCAGUGUGGGCUGGAAUAAAUAUG--------AGUAUGCACACAUACGGGUAUGUCUUUCUUUUCGGCCACUA
..(((((((..((((...))))...))))))).(((((...((((((.....)))))).((((...((((.--------.(((((....)))))..))))....)))).)))))...... ( -26.80)
>DroYak_CAF1 48284 102 + 1
CUUUGAACGCGUGCGCAACGCAACCUGUUUAAUCUGAAUUUGCUCACCCAAUGUGGGCUGGAAUACAUAUA--------UUUAUAUA----------UAUAUGUUCAUUUUCGGCUACUA
..(((((((..((((...))))...))))))).(((((...((((((.....))))))..(((((.(((((--------(....)))----------))).)))))...)))))...... ( -25.10)
>consensus
CUUUGAACGCGUGCGCAACGCAACCCGUUUAAUCUGAAUUUGCUCACCCAAUGUGGGCUGGAAUAUAUAUA________UUUAUAUA__________UAUAUAUUCAUUUUCGGCCACUA
..(((((((..((((...))))...)))))))............(((.....)))((((((((.(((((((..........................)))))))....)))))))).... (-21.13 = -20.45 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,976,992 – 6,977,095
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.54
Mean single sequence MFE -28.02
Consensus MFE -19.06
Energy contribution -18.62
Covariance contribution -0.44
Combinations/Pair 1.17
Mean z-score -2.26
Structure conservation index 0.68
SVM decision value 1.18
SVM RNA-class probability 0.926409
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6976992 103 + 23771897
UGCUCACUCAAUGUGGGCUGGAAUAUAUAU-------UAUAUGUAUA----------UAUAUAUUCAUUUUCGGCCACUAUCUGAUCGAUCGAAAGACAAUUAGCCAAAUAAGUCGACGG
.((((((.....))))))..((((((((((-------.........)----------)))))))))....(((((......(((((.(.((....))).)))))........)))))... ( -26.54)
>DroSim_CAF1 46678 110 + 1
UGUUCACUCAAUGUGGGCUGGAAUAUAUAUAUAUAUUGAUUUAUAUG----------UAUAUAUUCAUUUUCGGCCACUAUCUGAUCGAUCGAAAGACAAUUAGCCAAAUAAGUCGACGG
.((((((.....))))))..(((((((((((((((......))))))----------)))))))))....(((((......(((((.(.((....))).)))))........)))))... ( -31.44)
>DroEre_CAF1 46838 112 + 1
UGCUCACCCAGUGUGGGCUGGAAUAAAUAUG--------AGUAUGCACACAUACGGGUAUGUCUUUCUUUUCGGCCACUAUCUGAUCGAUCGAAAGACAAUUAGCCAAAUAAGUCGACGG
.((((((.....))))))(((.....((((.--------.(((((....)))))..))))(((((((...(((..((.....))..)))..)))))))......)))............. ( -29.70)
>DroYak_CAF1 48324 102 + 1
UGCUCACCCAAUGUGGGCUGGAAUACAUAUA--------UUUAUAUA----------UAUAUGUUCAUUUUCGGCUACUAUCCGAUCGAUCGAAAGACAAUUAGCCAAAUAAGUCGACGG
....(((.....)))((((((((.(((((((--------(......)----------)))))))....)))))))).....(((.((((((....))...(((......))).))))))) ( -24.40)
>consensus
UGCUCACCCAAUGUGGGCUGGAAUAUAUAUA________UUUAUAUA__________UAUAUAUUCAUUUUCGGCCACUAUCUGAUCGAUCGAAAGACAAUUAGCCAAAUAAGUCGACGG
....(((.....)))((((((((.(((((((..........................)))))))....)))))))).....(((.((((((....))...(((......))).))))))) (-19.06 = -18.62 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 6,976,992 – 6,977,095
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.54
Mean single sequence MFE -28.32
Consensus MFE -20.30
Energy contribution -20.36
Covariance contribution 0.06
Combinations/Pair 1.16
Mean z-score -2.64
Structure conservation index 0.72
SVM decision value 1.98
SVM RNA-class probability 0.984680
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6976992 103 - 23771897
CCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAUGAAUAUAUA----------UAUACAUAUA-------AUAUAUAUUCCAGCCCACAUUGAGUGAGCA
...........((((((((.((((((.((....))..))))))))))))))...(((((((((----------(.........-------))))))))))..((.(((.....))).)). ( -26.40)
>DroSim_CAF1 46678 110 - 1
CCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAUGAAUAUAUA----------CAUAUAAAUCAAUAUAUAUAUAUAUUCCAGCCCACAUUGAGUGAACA
..((..(((((((((((((.((((((.((....))..))))))))))))))...(((((((((----------.(((((......))))).)))))))))..........)))))..)). ( -28.80)
>DroEre_CAF1 46838 112 - 1
CCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAGAAAGACAUACCCGUAUGUGUGCAUACU--------CAUAUUUAUUCCAGCCCACACUGGGUGAGCA
..(((..(((.((((((((.((((((.((....))..)))))))))))))))))...))).((((((..((((.((.....--------.............)).)))).)))))).... ( -31.07)
>DroYak_CAF1 48324 102 - 1
CCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCGGAUAGUAGCCGAAAAUGAACAUAUA----------UAUAUAAA--------UAUAUGUAUUCCAGCCCACAUUGGGUGAGCA
.....(.(((.((((((((.((((((.((....))..)))))))))))))).....(((((((----------(......)--------)))))))......((((.....)))))))). ( -27.00)
>consensus
CCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAUGAAUAUAUA__________UAUAUAAA________UAUAUAUAUUCCAGCCCACAUUGAGUGAGCA
..((..(((((((((((((.((((((.((....))..))))))))))))))...(((((((((............................)))))))))..........)))))..)). (-20.30 = -20.36 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 6,977,025 – 6,977,135
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.96
Mean single sequence MFE -30.10
Consensus MFE -27.96
Energy contribution -27.02
Covariance contribution -0.94
Combinations/Pair 1.18
Mean z-score -1.30
Structure conservation index 0.93
SVM decision value 0.10
SVM RNA-class probability 0.582172
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6977025 110 - 23771897
AUUAAUUAAGACGCCGGCACGGGUACGAUCUCUCUGCUGCCCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAUGAAUAUAUA----------UAUACAU
.........((((.(((((.(((........))))))))..))))......((((((((.((((((.((....))..))))))))))))))............----------....... ( -27.90)
>DroSim_CAF1 46718 110 - 1
AUUAAUUAAGACGCCGGCACGGGUACGAUCUCUCUGCUGCCCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAUGAAUAUAUA----------CAUAUAA
.........((((.(((((.(((........))))))))..))))......((((((((.((((((.((....))..))))))))))))))............----------....... ( -27.90)
>DroEre_CAF1 46870 120 - 1
AUUAAUUAAGACGCCGGCACAGGUCGGAUCUCUCUGCUGCCCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAGAAAGACAUACCCGUAUGUGUGCAUAC
.........((((..((((((((.........)))).)))))))).........((.....((((((((..(((..((.....))..)))...))))))))...))(((((....))))) ( -32.40)
>DroYak_CAF1 48356 110 - 1
AUUAAUUGAGACGCGGGCACGGGUUCGAUCUCUCCGCUGUCCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCGGAUAGUAGCCGAAAAUGAACAUAUA----------UAUAUAA
......((((.((((((((((((.........)))).)))))).)).))))((((((((.((((((.((....))..))))))))))))))............----------....... ( -32.20)
>consensus
AUUAAUUAAGACGCCGGCACGGGUACGAUCUCUCUGCUGCCCGUCGACUUAUUUGGCUAAUUGUCUUUCGAUCGAUCAGAUAGUGGCCGAAAAUGAAUAUAUA__________UAUAUAA
.........((((..((((((((.........)))).))))))))......((((((((.((((((.((....))..))))))))))))))............................. (-27.96 = -27.02 +  -0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:29 2006